immunotation - Tools for working with diverse immune genes
MHC (major histocompatibility complex) molecules are cell
surface complexes that present antigens to T cells. The
repertoire of antigens presented in a given genetic background
largely depends on the sequence of the encoded MHC molecules,
and thus, in humans, on the highly variable HLA (human
leukocyte antigen) genes of the hyperpolymorphic HLA locus.
More than 28,000 different HLA alleles have been reported, with
significant differences in allele frequencies between human
populations worldwide. Reproducible and consistent annotation
of HLA alleles in large-scale bioinformatics workflows remains
challenging, because the available reference databases and
software tools often use different HLA naming schemes. The
package immunotation provides tools for consistent annotation
of HLA genes in typical immunoinformatics workflows such as for
example the prediction of MHC-presented peptides in different
human donors. Converter functions that provide mappings between
different HLA naming schemes are based on the MHC restriction
ontology (MRO). The package also provides automated access to
HLA alleles frequencies in worldwide human reference
populations stored in the Allele Frequency Net Database.
